From fe5ce40f710e797ee262fe638127d3372bf14e15 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 18 Feb 2025 09:52:13 +0100
Subject: [PATCH] Fixed some errors
---
src/outils.py | 2 ++
src/subworkflow.py | 6 ++----
src/workflow.py | 34 ++--------------------------------
3 files changed, 6 insertions(+), 36 deletions(-)
diff --git a/src/outils.py b/src/outils.py
index f1bb04f..4337c1a 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1318,6 +1318,7 @@ def get_channels_to_add_in_false_conditions(body, emitted_channels):
to_remove = []
for condition in tab:
#If the condition and it's neagtion are in the tab -> then we remove the condition and it's negation form the list
+ condition = condition.split("$$__$$")[0]
negation = f"!({condition})"
if(negation in tab):
to_remove.append(condition)
@@ -1328,6 +1329,7 @@ def get_channels_to_add_in_false_conditions(body, emitted_channels):
#For the remaining condition in the list -> need to create an empty channel in the case of the negation
for condition in channels_2_conditions[channel]:
+ condition = condition.split("$$__$$")[0]
body += f"\nif(!({condition})) {{\n{channel} = Channel.empty()\n}}"
return body
diff --git a/src/subworkflow.py b/src/subworkflow.py
index ee80322..c132338 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -64,12 +64,10 @@ class Subworkflow(Main):
for c in call.get_all_calls():
if(c.first_element_called.get_alias()==name):
tab.append(c)
-
-
#Here it is important that BioFlow-Insight is not a Nextflow verificator
#Here i'm checking the call inside the block
- if(len(tab)!=0):
- for c in self.root.get_calls_inside_level():
+ if(len(tab)==0):
+ for call in self.root.get_calls_inside_level():
#call.initialise()
for c in call.get_all_calls():
if(c.first_element_called.get_alias()==name):
diff --git a/src/workflow.py b/src/workflow.py
index fe2baf4..24b72fc 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -544,39 +544,9 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
param = parameters[i]
takes = subworkflow_takes[i].get_gives()[0]
#Here we're checking that the input inside and outside the subworkflow are the same
- #If they are we're going to remove everything to avoid the case
-
- """
- param_1 = fastq
- sub(param_1)
-
- AND in the subworkflow
-
- sub{
- take:
- fastq
- }
- ----------
- This would mean when removing the subworkflow def -> we would get this:
-
- param_1 = fastq
- fastq = param_1
- """
- #Obviously we want to avoid this case
- input_val = ""
- try:
- input_val = param.origins[0].get_source()[0].get_origins()[0].get_name()
- except:
- input_val = param.get_code(get_OG = True)
- if(takes.get_code()!=input_val):
+ if(takes.get_code()!=param.get_code(get_OG = True)):
new_header+=f"{takes.get_code()} = {param.get_code(get_OG = True)}"
- else:
- #In the case they are the same -> we remove the remaining operation (which doesn't serve a purpose)
- #The "param_1 = fastq" operation
- operation_code = param.origins[0].get_source()[0].get_code()
- code = code.replace(operation_code, "", 1)
-
-
+
code = code.replace(OG_call.get_code(get_OG = True), f"{new_header}\n\n{OG_body}", 1)
#REPLACE THE EMITS
--
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